AMAS

1. 官网

https://github.com/marekborowiec/AMAS/

2. 安装

PIP安装：https://pypi.org/project/amas/

AMAS是一个Python模块，要求Python版本为3.4及以上

3. 查看帮助文件

python3 绝对路径/AMAS.py -h

usage: AMAS <command> [<args>]

The AMAS commands are:
  concat      Concatenate input alignments
  convert     Convert to other file format
  replicate   Create replicate data sets for phylogenetic jackknife
  split       Split alignment according to a partitions file
  summary     Write alignment summary
  remove      Remove taxa from alignment
  translate   Translate DNA alignment into protein alignment
  trim        Remove columns from alignment

Use AMAS <command> -h for help with arguments of the command of interest

positional arguments:
  command     Subcommand to run

optional arguments:
  -h, --help  show this help message and exit

4. convert

fasta, phylip, nexus, phylip-int, nexus-int物种文件格式之间的互相转换

(RStudio-5) zhiyong@zhiyong-OptiPlex-7050:~/Application/anaconda3/envs/RStudio-5/lib/python3.8/site-packages/amas$ AMAS.py convert -h
usage: AMAS.py [-h] [-u {fasta,phylip,nexus,phylip-int,nexus-int}] [-e] [-c CORES] -i IN_FILES [IN_FILES ...] -f {fasta,phylip,nexus,phylip-int,nexus-int} -d {aa,dna}

Convert to other file format

optional arguments:
  -h, --help            show this help message and exit
  -u {fasta,phylip,nexus,phylip-int,nexus-int}, --out-format {fasta,phylip,nexus,phylip-int,nexus-int}
                        File format for the output alignment. Default: fasta
  -e, --check-align     Check if input sequences are aligned. Default: no check
  -c CORES, --cores CORES
                        Number of cores used. Default: 1

required arguments:
  -i IN_FILES [IN_FILES ...], --in-files IN_FILES [IN_FILES ...]
                        Alignment files to be taken as input. You can specify multiple files using wildcards (e.g. --in-files *fasta)
  -f {fasta,phylip,nexus,phylip-int,nexus-int}, --in-format {fasta,phylip,nexus,phylip-int,nexus-int}
                        The format of input alignment
  -d {aa,dna}, --data-type {aa,dna}
                        Type of data

4.1 将fasta转换成phylip

python3 绝对路径/AMAS.py convert -d dna -f fasta -i alihment.fasta -u phylip

• 1. dna: 输入文件的类型，aa或者dna
• 2. -f: 输入文件的格式
• 3. -i: 输入文件的文件名
• 4. -u: 输出文件的格式

输出文件的文件名由程序生成，即在输入文件的文件名后添加-out.输出文件格式缩写